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From: Neateye <nit...@ao...> - 2005-04-20 01:05:09
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Call out Gouranga be happy!!! Gouranga Gouranga Gouranga .... That which brings the highest happiness!! |
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From: Amruta J. <am...@st...> - 2005-04-20 00:09:53
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Hi, I've successfully installed GUS and am trying to load data into it. I have downloaded Bordetella bronchiseptica ds-DNA sequence in XML = format from: (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=3DNucleotide&cmd=3Dsear= ch&term=3Dnc_002927) I tried using LoadGeneFeatureFromXML (v1.878) plugin, but it prints the = length of submitted sequence as 0.=20 My guess is that the plugin is not able to parse my xml file.=20 Is TIGR XML format different from the Genbank XML file format? Is there some other plugin that parses xml to load data?=20 I tried using GBParser on data downloaded from the same site in GenBank = (.gb) format. That too failed with the error:=20 ------------------ entry number 1 ----------------- You have exceeded the maximum number of allowable objects in memory: ------------------ entry number 2 ----------------- Can't call method "getAccession" on an undefined value=20 The complete command and errors are pasted below for reference. thanks, Amruta LoadGeneFeatureFromXML: (Problem-Submitting sequence of length 0) [amrutaj@asiago gus]$ ga GUS::Common::Plugin::LoadGeneFeaturesFromXML = --XmlFile=3D"~/genbank_files/nc_002927.xml" \ > --Taxon=3D"Bordetella bronchiseptica RB50" --Project=3D"Bordetella = bronchiseptica RB50" --SeqTypeID=3D3 \ > --Algorithm=3DGUS::Common::Plugin::LoadGeneFeaturesFromXML = --extDbRelId=3D5004 -commit Tue Apr 19 10:03:14 2005 Finding Algorithm Tue Apr 19 10:03:14 2005 Finding Project Tue Apr 19 10:03:14 2005 Finding ExternalDatabaseReleaseId Tue Apr 19 10:03:14 2005 Finding ExternalDatabaseId Tue Apr 19 10:03:14 2005 Finding Sequence Type Id Tue Apr 19 10:03:14 2005 Loading XML = file/home/amrutaj/genbank_files/nc_002927.xml Loading XML file: /home/amrutaj/genbank_files/nc_002927.xml Tue Apr 19 10:04:51 2005 Finding TaxonID Submitting sequence of length 0 Tue Apr 19 10:05:19 2005 RESULT 1 [amrutaj@asiago gus]$=20 GBParser: ga GUS::Common::Plugin::GBParser \ --file=3D~/genbank_files/nc_002927.gb --debug \ --gbRel=3D146 --db_rel_id=3D22 --commit=20 ------------------ entry number 1 ----------------- You have exceeded the maximum number of allowable objects in memory: You must use the method 'undefPointerCache()' in each loop to clear the cache and allow garbage collection!! If you need > 50000 objects at one time, then increase the default number with the method = 'setMaximumNumberOfObjects(<number>)' at = /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 512 = GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=3D= HASH(0x8c371f8)','GUS::Model::DoTS::DbRefNASequence=3DHASH(0x12509d6c)') = called at /opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 28 GUS::Model::GusRow::new('GUS::Model::DoTS::DbRefNASequence') = called at /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line = 779 = GUS::Common::Plugin::GBParser::buildDbXRef('CBIL::Bio::GenBank::Qualifier= =3DHASH(0xbfd4144)','GUS::Model::DoTS::ExternalNASequence=3DHASH(0xdee73b= 8)') called at /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm = line 503 = GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBPars= er=3DHASH(0x85a0b90)','CBIL::Bio::GenBank::Entry=3DHASH(0xa374394)','GUS:= :Model::DoTS::ExternalNASequence=3DHASH(0xdee73b8)') called at = /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 251 = GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParse= r=3DHASH(0x85a0b90)','CBIL::Bio::GenBank::ArrayStream=3DHASH(0xa374328)')= called at /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line = 185 eval {...} called at = /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184 = GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=3DHASH(= 0x85a0b90)','HASH(0x8e4c168)') called at = /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 453 eval {...} called at = /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450 = GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::= GusApplication=3DHASH(0x804c8c4)','GUS::Common::Plugin::GBParser',1) = called at /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm = line 383 = GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli= cation=3DHASH(0x804c8c4)','GUS::Common::Plugin::GBParser') called at = /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 289 = GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati= on=3DHASH(0x804c8c4)','GUS::Common::Plugin::GBParser') called at = /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198 = GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati= on=3DHASH(0x804c8c4)','ARRAY(0x805ff68)') called at = /opt/gus/gus_home/bin/ga line 11 ------------------ entry number 2 ----------------- Can't call method "getAccession" on an undefined value at = /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 218, = <GEN0> line 230365. -------------------------------------------------------------------------= ---------------------------------------------------------------- |
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From: Jeetendra S. <so...@vb...> - 2005-04-19 19:06:52
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Hi all, I am loading some Blast results using LoadBlastSimFast plugin. There's a slight problem in loading the subjects/hsps when the evalue is 0. When the evalue is 0, the plugin loads mantissa and exponent values as 1. In the source code, it splits the e-value string using 'e' as the delimiter, and when the values are not initialized (or they are 0), it defaults both mantissa and exponent to 1. Any comments/thoughts would be appreciated. Thanks, Jeetendra. |
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From: Michael S. <msa...@pc...> - 2005-04-07 17:54:07
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All, Development work on the GUS 3.5 Schema is nearing completion, and we'd like to take this opportunity to solicit community feedback and provide the 3.5 schema for review. With the 3.5 Schema nearly finalized, we're now turning our attention to ensuring compatibility in the object layer and with plugins for 3.5. Once done, GUS 3.5 will be ready for release. It's my hope that that will be as soon as possible, but I'm hesitant to give a firm date. The attached file contains the 3.5 schema, in a simple text summary format. When reviewing the file, please keep the following in mind: * I've done a very preliminary analysis of the file--- there may be glaring mistakes/omissions. * All tables and views in GUS 3.5 are versioned, and the version tables/views are not displayed. * All tables and views in GUS 3.5 contain the standard housekeeping columns, which are also not displayed. * Subclass tables (marked by "extends superclass" where superclass is the name of the parent table) only have the columns added by the subclass displayed. For example, if the superclass has columns a, b, c, and d, then the subclass will display the column e but have all five columns in the database. * This is an object-centric display-- the method of subclassing (i.e. use of imp tables) is not changing. As a result, Imp tables are not displayed, nor are super/sub classes flagged as views. * The Type of a column with a foreign key is the name of the foreign key table. For example, a table with a column NA_FEATURE_ID with a foreign key to DoTS.NAFEATURE will have a type of DoTSS.NAFEATURE. This is the only way foreign keys are displayed in this view. * All tables first column serves as the Primary key. There is no denotation for the primary key (although it will also appear as an index against the first column). Some tables are missing primary keys in this document-- it will be fixed soon. * All indexes for a table are displayed. Please let me know if you have any questions/concerns. Thanks, Mike |
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From: Steve F. <sfi...@pc...> - 2005-04-06 14:23:46
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federica- maybe your ojdbc14_g.jar contains the xerxes classes (they would conflict with xercesImpl.jar) to find out, do this: % jar -tf $GUS_HOME/lib/java/ojdbc14_g.jar it will show you the class files in the jar. see if any of the xerces classes are in there. if they are, that is the problem. steve fed...@bi... wrote: >Hi Steve, I cleaned the directory and run the build command again, but >nothing...the wdkXml doesen't work! Always the same problem about >xercesImpl.jar. >In my $GUS_HOME/lib/java directory now there are these jars: >commons-beanutils.jar >commons-cli-1.0.jar >commons-collections.jar >commons-dbcp-1.1.jar >commons-digester-1.5.jar >commons-logging-api.jar >commons-pool-1.1.jar >jing-20030619.jar >jstl.jar >jsp-api-2.0.jar >ojdbc14_g.jar >pager-taglib.jar >servlet-api-2.4.jar >standard.jar >struts-1.1.jar >WDK-Model.jar >WDK-Controller.jar >xercesImpl.jar >xml-apis.jar >wraptag.jar > >The differences with yours are that I use ojdbc and I haven't >oracle-classes, I have wraptag and I miss WDK-View.jar. > >Any other idea about why my test doesn't work?? >Thank, >Federica > > > > > > >>the jars the wdk needs are: >> >>commons-beanutils.jar >>commons-cli-1.0.jar >>commons-collections.jar >>commons-dbcp-1.1.jar >>commons-digester-1.5.jar >>commons-logging-api.jar >>commons-pool-1.1.jar >>jing-20030619.jar >>jsp-api-2.0.jar >>jstl.jar >>oracle-classes12.jar >>pager-taglib.jar >>servlet-api-2.4.jar >>standard.jar >>struts-1.1.jar >>WDK-Controller.jar >>WDK-Model.jar >>WDK-View.jar >>xercesImpl.jar >>xml-apis.jar >> >> >>fed...@bi... wrote: >> >> >> >>>Hi everyone! >>>Steve, I empty my classpath but it doesn't work! >>>In my $GUS_HOME/lib/java directory there are these jars: >>>biojava.jar commons-collections.jar commons-pool-1.1.jar >>>jing-20030619.jar oracle-classes12.jar provaClasse.java >>>WDK-Controller.jar xml-apis.jar >>>CBIL-CSP.jar commons-dbcp-1.1.jar GUS-GOPredict.jar >>>jsp-api-2.0.jar pager-taglib.jar servlet-api-2.4.jar >>>WDK-Model.jar >>>commons-beanutils.jar commons-digester-1.5.jar GUS-Model.jar >>>jstl.jar PerlTools-1.2.jar standard.jar wraptag.jar >>>commons-cli-1.0.jar commons-logging-api.jar GUS-ObjRelJ.jar >>>ojdbc14_g.jar provaClasse.class struts-1.1.jar >>>xercesImpl.jar >>> >>>Do you think it could be a problem of xercesImpl.jar version? >>>Thanks, >>>Federica >>> >>> >>> >>> >>> >>>>federica- >>>> >>>>1.4 is required. >>>> >>>>i believe the problem is that there is another version of xerces in the >>>>classpath somehow. >>>> >>>>did you make sure CLASSPATH was empty? >>>> >>>>can you do this, and send the result: >>>> >>>>% ls $GUS_HOME/lib/java >>>> >>>>steve >>>> >>>>fed...@bi... wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Hi guys! >>>>>My problem with wdkXml has not been solved yet! Thanks Steve for your >>>>>advice! >>>>>Now my question is: with GUS WDK 1.2 the requirements of Gus are always >>>>>the same? >>>>>In particular, what is the j2sdk version required? >>>>>Thanks everyone, >>>>>Federica >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>federica- >>>>>> >>>>>>the wdk does not need the CLASSPATH to be set. the build takes care >>>>>>of >>>>>>that. try emptying your CLASSPATH >>>>>> >>>>>>steve >>>>>> >>>>>>fed...@bi... wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Hi! It's Federica here, I wrote you in the past! >>>>>>>I'm fighting with the wdk model (WDK 1.2)! When I run this command: >>>>>>>wdkXml -model toyModel >>>>>>> >>>>>>>it gives me this java class error: >>>>>>>.Exception in thread "main" java.lang.NoSuchMethodError: >>>>>>>org.apache.xerces.parser >>>>>>>s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >>>>>>>nt;)V >>>>>>> at >>>>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>>>Source) >>>>>>> at >>>>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>>>Source) >>>>>>> at >>>>>>>sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>>>>>>Method) >>>>>>> at >>>>>>>sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >>>>>>>orAccessorImpl.java:39) >>>>>>> at >>>>>>>sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >>>>>>>onstructorAccessorImpl.java:27) >>>>>>> at >>>>>>>java.lang.reflect.Constructor.newInstance(Constructor.java:274) >>>>>>> at java.lang.Class.newInstance0(Class.java:308) >>>>>>> at java.lang.Class.newInstance(Class.java:261) >>>>>>> at >>>>>>>org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 >>>>>>> 07) >>>>>>> at >>>>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>>>> 177) >>>>>>> at >>>>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>>>> 137) >>>>>>> at >>>>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) >>>>>>> at >>>>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) >>>>>>> at >>>>>>>org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) >>>>>>> at >>>>>>>org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac >>>>>>> toryImpl.java:95) >>>>>>> at >>>>>>>com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk >>>>>>> nown Source) >>>>>>> at >>>>>>>com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow >>>>>>> n Source) >>>>>>> at >>>>>>>com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >>>>>>>Sourc e) >>>>>>> at >>>>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode >>>>>>> lXmlParser.java:184) >>>>>>> at >>>>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX >>>>>>> mlParser.java:71) >>>>>>> at >>>>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser >>>>>>> .java:412) >>>>>>> >>>>>>>I think my classpath is correct. In it I specified the path of >>>>>>>xercesImpl.jar that should be the archive of my class. >>>>>>>Can anyone help me? >>>>>>>Thanks >>>>>>>Federica >>>>>>> >>>>>>> >>>>>>> >>>>>>>------------------------------------------------------- >>>>>>>This SF.net email is sponsored by Demarc: >>>>>>>A global provider of Threat Management Solutions. >>>>>>>Download our HomeAdmin security software for free today! >>>>>>>http://www.demarc.com/Info/Sentarus/hamr30 >>>>>>>_______________________________________________ >>>>>>>Gusdev-gusdev mailing list >>>>>>>Gus...@li... >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > > |
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From: <fed...@bi...> - 2005-04-06 09:40:57
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Hi Steve, I cleaned the directory and run the build command again, but nothing...the wdkXml doesen't work! Always the same problem about xercesImpl.jar. In my $GUS_HOME/lib/java directory now there are these jars: commons-beanutils.jar commons-cli-1.0.jar commons-collections.jar commons-dbcp-1.1.jar commons-digester-1.5.jar commons-logging-api.jar commons-pool-1.1.jar jing-20030619.jar jstl.jar jsp-api-2.0.jar ojdbc14_g.jar pager-taglib.jar servlet-api-2.4.jar standard.jar struts-1.1.jar WDK-Model.jar WDK-Controller.jar xercesImpl.jar xml-apis.jar wraptag.jar The differences with yours are that I use ojdbc and I haven't oracle-classes, I have wraptag and I miss WDK-View.jar. Any other idea about why my test doesn't work?? Thank, Federica > the jars the wdk needs are: > > commons-beanutils.jar > commons-cli-1.0.jar > commons-collections.jar > commons-dbcp-1.1.jar > commons-digester-1.5.jar > commons-logging-api.jar > commons-pool-1.1.jar > jing-20030619.jar > jsp-api-2.0.jar > jstl.jar > oracle-classes12.jar > pager-taglib.jar > servlet-api-2.4.jar > standard.jar > struts-1.1.jar > WDK-Controller.jar > WDK-Model.jar > WDK-View.jar > xercesImpl.jar > xml-apis.jar > > > fed...@bi... wrote: > >>Hi everyone! >>Steve, I empty my classpath but it doesn't work! >>In my $GUS_HOME/lib/java directory there are these jars: >>biojava.jar commons-collections.jar commons-pool-1.1.jar >>jing-20030619.jar oracle-classes12.jar provaClasse.java >>WDK-Controller.jar xml-apis.jar >>CBIL-CSP.jar commons-dbcp-1.1.jar GUS-GOPredict.jar >>jsp-api-2.0.jar pager-taglib.jar servlet-api-2.4.jar >>WDK-Model.jar >>commons-beanutils.jar commons-digester-1.5.jar GUS-Model.jar >>jstl.jar PerlTools-1.2.jar standard.jar wraptag.jar >>commons-cli-1.0.jar commons-logging-api.jar GUS-ObjRelJ.jar >>ojdbc14_g.jar provaClasse.class struts-1.1.jar >>xercesImpl.jar >> >>Do you think it could be a problem of xercesImpl.jar version? >>Thanks, >>Federica >> >> >> >>>federica- >>> >>>1.4 is required. >>> >>>i believe the problem is that there is another version of xerces in the >>>classpath somehow. >>> >>>did you make sure CLASSPATH was empty? >>> >>>can you do this, and send the result: >>> >>>% ls $GUS_HOME/lib/java >>> >>>steve >>> >>>fed...@bi... wrote: >>> >>> >>> >>>>Hi guys! >>>>My problem with wdkXml has not been solved yet! Thanks Steve for your >>>>advice! >>>>Now my question is: with GUS WDK 1.2 the requirements of Gus are always >>>>the same? >>>>In particular, what is the j2sdk version required? >>>>Thanks everyone, >>>>Federica >>>> >>>> >>>> >>>> >>>> >>>>>federica- >>>>> >>>>>the wdk does not need the CLASSPATH to be set. the build takes care >>>>> of >>>>>that. try emptying your CLASSPATH >>>>> >>>>>steve >>>>> >>>>>fed...@bi... wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Hi! It's Federica here, I wrote you in the past! >>>>>>I'm fighting with the wdk model (WDK 1.2)! When I run this command: >>>>>>wdkXml -model toyModel >>>>>> >>>>>>it gives me this java class error: >>>>>>.Exception in thread "main" java.lang.NoSuchMethodError: >>>>>>org.apache.xerces.parser >>>>>>s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >>>>>>nt;)V >>>>>> at >>>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>>Source) >>>>>> at >>>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>>Source) >>>>>> at >>>>>> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>>>>>Method) >>>>>> at >>>>>>sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >>>>>>orAccessorImpl.java:39) >>>>>> at >>>>>>sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >>>>>>onstructorAccessorImpl.java:27) >>>>>> at >>>>>>java.lang.reflect.Constructor.newInstance(Constructor.java:274) >>>>>> at java.lang.Class.newInstance0(Class.java:308) >>>>>> at java.lang.Class.newInstance(Class.java:261) >>>>>> at >>>>>>org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 >>>>>> 07) >>>>>> at >>>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>>> 177) >>>>>> at >>>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>>> 137) >>>>>> at >>>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) >>>>>> at >>>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) >>>>>> at >>>>>>org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) >>>>>> at >>>>>>org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac >>>>>> toryImpl.java:95) >>>>>> at >>>>>>com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk >>>>>> nown Source) >>>>>> at >>>>>>com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow >>>>>> n Source) >>>>>> at >>>>>>com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >>>>>>Sourc e) >>>>>> at >>>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode >>>>>> lXmlParser.java:184) >>>>>> at >>>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX >>>>>> mlParser.java:71) >>>>>> at >>>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser >>>>>> .java:412) >>>>>> >>>>>>I think my classpath is correct. In it I specified the path of >>>>>>xercesImpl.jar that should be the archive of my class. >>>>>>Can anyone help me? >>>>>>Thanks >>>>>>Federica >>>>>> >>>>>> >>>>>> >>>>>>------------------------------------------------------- >>>>>>This SF.net email is sponsored by Demarc: >>>>>>A global provider of Threat Management Solutions. >>>>>>Download our HomeAdmin security software for free today! >>>>>>http://www.demarc.com/Info/Sentarus/hamr30 >>>>>>_______________________________________________ >>>>>>Gusdev-gusdev mailing list >>>>>>Gus...@li... >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >> >> >> > |
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From: Steve F. <sfi...@pc...> - 2005-04-05 16:08:37
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the jars the wdk needs are: commons-beanutils.jar commons-cli-1.0.jar commons-collections.jar commons-dbcp-1.1.jar commons-digester-1.5.jar commons-logging-api.jar commons-pool-1.1.jar jing-20030619.jar jsp-api-2.0.jar jstl.jar oracle-classes12.jar pager-taglib.jar servlet-api-2.4.jar standard.jar struts-1.1.jar WDK-Controller.jar WDK-Model.jar WDK-View.jar xercesImpl.jar xml-apis.jar fed...@bi... wrote: >Hi everyone! >Steve, I empty my classpath but it doesn't work! >In my $GUS_HOME/lib/java directory there are these jars: >biojava.jar commons-collections.jar commons-pool-1.1.jar >jing-20030619.jar oracle-classes12.jar provaClasse.java >WDK-Controller.jar xml-apis.jar >CBIL-CSP.jar commons-dbcp-1.1.jar GUS-GOPredict.jar >jsp-api-2.0.jar pager-taglib.jar servlet-api-2.4.jar >WDK-Model.jar >commons-beanutils.jar commons-digester-1.5.jar GUS-Model.jar >jstl.jar PerlTools-1.2.jar standard.jar wraptag.jar >commons-cli-1.0.jar commons-logging-api.jar GUS-ObjRelJ.jar >ojdbc14_g.jar provaClasse.class struts-1.1.jar >xercesImpl.jar > >Do you think it could be a problem of xercesImpl.jar version? >Thanks, >Federica > > > >>federica- >> >>1.4 is required. >> >>i believe the problem is that there is another version of xerces in the >>classpath somehow. >> >>did you make sure CLASSPATH was empty? >> >>can you do this, and send the result: >> >>% ls $GUS_HOME/lib/java >> >>steve >> >>fed...@bi... wrote: >> >> >> >>>Hi guys! >>>My problem with wdkXml has not been solved yet! Thanks Steve for your >>>advice! >>>Now my question is: with GUS WDK 1.2 the requirements of Gus are always >>>the same? >>>In particular, what is the j2sdk version required? >>>Thanks everyone, >>>Federica >>> >>> >>> >>> >>> >>>>federica- >>>> >>>>the wdk does not need the CLASSPATH to be set. the build takes care of >>>>that. try emptying your CLASSPATH >>>> >>>>steve >>>> >>>>fed...@bi... wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Hi! It's Federica here, I wrote you in the past! >>>>>I'm fighting with the wdk model (WDK 1.2)! When I run this command: >>>>>wdkXml -model toyModel >>>>> >>>>>it gives me this java class error: >>>>>.Exception in thread "main" java.lang.NoSuchMethodError: >>>>>org.apache.xerces.parser >>>>>s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >>>>>nt;)V >>>>> at >>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>Source) >>>>> at >>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>Source) >>>>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>>>>Method) >>>>> at >>>>>sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >>>>>orAccessorImpl.java:39) >>>>> at >>>>>sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >>>>>onstructorAccessorImpl.java:27) >>>>> at >>>>>java.lang.reflect.Constructor.newInstance(Constructor.java:274) >>>>> at java.lang.Class.newInstance0(Class.java:308) >>>>> at java.lang.Class.newInstance(Class.java:261) >>>>> at >>>>>org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 >>>>> 07) >>>>> at >>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>> 177) >>>>> at >>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>> 137) >>>>> at >>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) >>>>> at >>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) >>>>> at >>>>>org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) >>>>> at >>>>>org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac >>>>> toryImpl.java:95) >>>>> at >>>>>com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk >>>>> nown Source) >>>>> at >>>>>com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow >>>>> n Source) >>>>> at >>>>>com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >>>>>Sourc e) >>>>> at >>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode >>>>> lXmlParser.java:184) >>>>> at >>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX >>>>> mlParser.java:71) >>>>> at >>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser >>>>> .java:412) >>>>> >>>>>I think my classpath is correct. In it I specified the path of >>>>>xercesImpl.jar that should be the archive of my class. >>>>>Can anyone help me? >>>>>Thanks >>>>>Federica >>>>> >>>>> >>>>> >>>>>------------------------------------------------------- >>>>>This SF.net email is sponsored by Demarc: >>>>>A global provider of Threat Management Solutions. >>>>>Download our HomeAdmin security software for free today! >>>>>http://www.demarc.com/Info/Sentarus/hamr30 >>>>>_______________________________________________ >>>>>Gusdev-gusdev mailing list >>>>>Gus...@li... >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > > |
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From: Steve F. <sfi...@pc...> - 2005-04-05 16:00:24
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federica- remove all the .jar files from your $GUS_HOME/lib/java and do a build again. it is possible that one of those jar files contains an old version of xerces. the build will put in there exactly the jar files needed by the wdk. steve fed...@bi... wrote: >Hi everyone! >Steve, I empty my classpath but it doesn't work! >In my $GUS_HOME/lib/java directory there are these jars: >biojava.jar commons-collections.jar commons-pool-1.1.jar >jing-20030619.jar oracle-classes12.jar provaClasse.java >WDK-Controller.jar xml-apis.jar >CBIL-CSP.jar commons-dbcp-1.1.jar GUS-GOPredict.jar >jsp-api-2.0.jar pager-taglib.jar servlet-api-2.4.jar >WDK-Model.jar >commons-beanutils.jar commons-digester-1.5.jar GUS-Model.jar >jstl.jar PerlTools-1.2.jar standard.jar wraptag.jar >commons-cli-1.0.jar commons-logging-api.jar GUS-ObjRelJ.jar >ojdbc14_g.jar provaClasse.class struts-1.1.jar >xercesImpl.jar > >Do you think it could be a problem of xercesImpl.jar version? >Thanks, >Federica > > > >>federica- >> >>1.4 is required. >> >>i believe the problem is that there is another version of xerces in the >>classpath somehow. >> >>did you make sure CLASSPATH was empty? >> >>can you do this, and send the result: >> >>% ls $GUS_HOME/lib/java >> >>steve >> >>fed...@bi... wrote: >> >> >> >>>Hi guys! >>>My problem with wdkXml has not been solved yet! Thanks Steve for your >>>advice! >>>Now my question is: with GUS WDK 1.2 the requirements of Gus are always >>>the same? >>>In particular, what is the j2sdk version required? >>>Thanks everyone, >>>Federica >>> >>> >>> >>> >>> >>>>federica- >>>> >>>>the wdk does not need the CLASSPATH to be set. the build takes care of >>>>that. try emptying your CLASSPATH >>>> >>>>steve >>>> >>>>fed...@bi... wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Hi! It's Federica here, I wrote you in the past! >>>>>I'm fighting with the wdk model (WDK 1.2)! When I run this command: >>>>>wdkXml -model toyModel >>>>> >>>>>it gives me this java class error: >>>>>.Exception in thread "main" java.lang.NoSuchMethodError: >>>>>org.apache.xerces.parser >>>>>s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >>>>>nt;)V >>>>> at >>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>Source) >>>>> at >>>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>>Source) >>>>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>>>>Method) >>>>> at >>>>>sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >>>>>orAccessorImpl.java:39) >>>>> at >>>>>sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >>>>>onstructorAccessorImpl.java:27) >>>>> at >>>>>java.lang.reflect.Constructor.newInstance(Constructor.java:274) >>>>> at java.lang.Class.newInstance0(Class.java:308) >>>>> at java.lang.Class.newInstance(Class.java:261) >>>>> at >>>>>org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 >>>>> 07) >>>>> at >>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>> 177) >>>>> at >>>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>>> 137) >>>>> at >>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) >>>>> at >>>>>org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) >>>>> at >>>>>org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) >>>>> at >>>>>org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac >>>>> toryImpl.java:95) >>>>> at >>>>>com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk >>>>> nown Source) >>>>> at >>>>>com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow >>>>> n Source) >>>>> at >>>>>com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >>>>>Sourc e) >>>>> at >>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode >>>>> lXmlParser.java:184) >>>>> at >>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX >>>>> mlParser.java:71) >>>>> at >>>>>org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser >>>>> .java:412) >>>>> >>>>>I think my classpath is correct. In it I specified the path of >>>>>xercesImpl.jar that should be the archive of my class. >>>>>Can anyone help me? >>>>>Thanks >>>>>Federica >>>>> >>>>> >>>>> >>>>>------------------------------------------------------- >>>>>This SF.net email is sponsored by Demarc: >>>>>A global provider of Threat Management Solutions. >>>>>Download our HomeAdmin security software for free today! >>>>>http://www.demarc.com/Info/Sentarus/hamr30 >>>>>_______________________________________________ >>>>>Gusdev-gusdev mailing list >>>>>Gus...@li... >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > > |
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From: <fed...@bi...> - 2005-04-05 13:38:04
|
Hi everyone! Steve, I empty my classpath but it doesn't work! In my $GUS_HOME/lib/java directory there are these jars: biojava.jar commons-collections.jar commons-pool-1.1.jar jing-20030619.jar oracle-classes12.jar provaClasse.java WDK-Controller.jar xml-apis.jar CBIL-CSP.jar commons-dbcp-1.1.jar GUS-GOPredict.jar jsp-api-2.0.jar pager-taglib.jar servlet-api-2.4.jar WDK-Model.jar commons-beanutils.jar commons-digester-1.5.jar GUS-Model.jar jstl.jar PerlTools-1.2.jar standard.jar wraptag.jar commons-cli-1.0.jar commons-logging-api.jar GUS-ObjRelJ.jar ojdbc14_g.jar provaClasse.class struts-1.1.jar xercesImpl.jar Do you think it could be a problem of xercesImpl.jar version? Thanks, Federica > federica- > > 1.4 is required. > > i believe the problem is that there is another version of xerces in the > classpath somehow. > > did you make sure CLASSPATH was empty? > > can you do this, and send the result: > > % ls $GUS_HOME/lib/java > > steve > > fed...@bi... wrote: > >>Hi guys! >>My problem with wdkXml has not been solved yet! Thanks Steve for your >> advice! >>Now my question is: with GUS WDK 1.2 the requirements of Gus are always >>the same? >>In particular, what is the j2sdk version required? >>Thanks everyone, >>Federica >> >> >> >>>federica- >>> >>>the wdk does not need the CLASSPATH to be set. the build takes care of >>>that. try emptying your CLASSPATH >>> >>>steve >>> >>>fed...@bi... wrote: >>> >>> >>> >>>>Hi! It's Federica here, I wrote you in the past! >>>>I'm fighting with the wdk model (WDK 1.2)! When I run this command: >>>>wdkXml -model toyModel >>>> >>>>it gives me this java class error: >>>>.Exception in thread "main" java.lang.NoSuchMethodError: >>>>org.apache.xerces.parser >>>>s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >>>>nt;)V >>>> at >>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>Source) >>>> at >>>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>>Source) >>>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>>>Method) >>>> at >>>>sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >>>>orAccessorImpl.java:39) >>>> at >>>>sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >>>>onstructorAccessorImpl.java:27) >>>> at >>>>java.lang.reflect.Constructor.newInstance(Constructor.java:274) >>>> at java.lang.Class.newInstance0(Class.java:308) >>>> at java.lang.Class.newInstance(Class.java:261) >>>> at >>>>org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 >>>> 07) >>>> at >>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>> 177) >>>> at >>>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>>> 137) >>>> at >>>> org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) >>>> at >>>> org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) >>>> at >>>>org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) >>>> at >>>>org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac >>>> toryImpl.java:95) >>>> at >>>>com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk >>>> nown Source) >>>> at >>>>com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow >>>> n Source) >>>> at >>>>com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >>>>Sourc e) >>>> at >>>>org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode >>>> lXmlParser.java:184) >>>> at >>>>org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX >>>> mlParser.java:71) >>>> at >>>>org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser >>>> .java:412) >>>> >>>>I think my classpath is correct. In it I specified the path of >>>>xercesImpl.jar that should be the archive of my class. >>>>Can anyone help me? >>>>Thanks >>>>Federica >>>> >>>> >>>> >>>>------------------------------------------------------- >>>>This SF.net email is sponsored by Demarc: >>>>A global provider of Threat Management Solutions. >>>>Download our HomeAdmin security software for free today! >>>>http://www.demarc.com/Info/Sentarus/hamr30 >>>>_______________________________________________ >>>>Gusdev-gusdev mailing list >>>>Gus...@li... >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >>>> >> >> >> > |
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From: Sucheta T. <su...@vb...> - 2005-04-05 13:15:32
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Hi Steve, The query is cgi based except for the advanced query.Other than that boolean, history are part of wdk classic. Toolkit is agin our own, based on PHP. Since the servlet blast was slower, I implemented this one, which is much faster. I think we can work together to release this part of frontend, as additional package if the users are interested. -Sucheta > sucheta- > > i looked at the site. wow, that's great!!! > > as i look at it, it seems that the querying, history, boolean and > toolkit seem to be WDK-Classic. Is that right? > > It looks like the Annotate is cgi. (i look forward to hearing from you > how you made this part). > > As i mentioned in previous mail, cryptodb will be coming live any day > now, and you can see the new WDK. (it doesn't have history yet). > But, it should be very easy for you to transition the querying and > boolean to the new wdk. the new wdk is much, much easier to use, and > is already starting to show its power. the cryptodb team developed a > GBrowse adaptor so that GBrowse is easy to use with it. > > steve > > > Sucheta Tripathy wrote: > >>Hi Alberto, >> >>We had wdk classic installed for the frontend, but somehow we could not >>make it work the way we wanted. So we built our cgi based browser, and >>other accessories.We still have wdk classic for certain things like >>boolean/advanced query and history, but I may still need to work on those >>to make them fully functional. We are currently into modularising the >>components of the browser, so that it can be easily implemented for >>different applications.Then it will be released for distribution. >> >>Sucheta >> >> >> >>>Hi Sucheta, >>> >>>Congrats on the site and DB, looks great. >>> >>>So, looks like you have used (built) a CGI-based browser instead using >>>the WDK (we have been unable to have it completely debugged for the GUS- >>>Postgres)... did you give any try to WDK and the GUS-Postgres ? >>> >>>Looking forward to the public release of your browser. >>> >>>Cheers, Alberto >>> >>> >>>On Mon, 2005-04-04 at 16:11 -0400, Sucheta Tripathy wrote: >>> >>> >>>>Dear Group, >>>> >>>>I just wanted to inform you that we have released our phytophthraDB >>>>based >>>>on GUS. Steve, if you would like to mention in your paper. >>>> >>>>We have built a brand new browser on the top of GUS database and also >>>>have >>>>lots of additional features including a community annotation interface. >>>>You >>>>may check it out at: >>>> >>>>http://phytophthora.vbi.vt.edu/ >>>> >>>>The browser will be shortly released after licensing. Thank you all for >>>>the >>>>support. >>>> >>>>Sucheta >>>> >>>>At 10:45 AM 4/4/2005 -0400, Steve Fischer wrote: >>>> >>>> >>>>>GUS users- >>>>> >>>>>Attached is a draft of a paper describing the GUS system. We have not >>>>> >>>>> >>>>yet >>>> >>>> >>>>>finalized what journal we'll be submitting it to. >>>>> >>>>>We would like your feedback on the paper before we submit it. >>>>> >>>>>Also, there is a chart in the paper describing GUS users. Please >>>>> >>>>> >>>>confirm >>>> >>>> >>>>>the information there that is pertinent to you. If you are not in >>>>> the >>>>>chart and would like to be, please provide the necessary information. >>>>> >>>>> >>>>If >>>> >>>> >>>>>you are on the chart and would like to be removed, please let me know. >>>>> >>>>>Thanks in advance for your feedback, >>>>>Steve >>>>> >>>>> >>>>> >>>>> >> >> >> >> > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
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From: Steve F. <sfi...@pc...> - 2005-04-05 13:06:08
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sucheta- i looked at the site. wow, that's great!!! as i look at it, it seems that the querying, history, boolean and toolkit seem to be WDK-Classic. Is that right? It looks like the Annotate is cgi. (i look forward to hearing from you how you made this part). As i mentioned in previous mail, cryptodb will be coming live any day now, and you can see the new WDK. (it doesn't have history yet). But, it should be very easy for you to transition the querying and boolean to the new wdk. the new wdk is much, much easier to use, and is already starting to show its power. the cryptodb team developed a GBrowse adaptor so that GBrowse is easy to use with it. steve Sucheta Tripathy wrote: >Hi Alberto, > >We had wdk classic installed for the frontend, but somehow we could not >make it work the way we wanted. So we built our cgi based browser, and >other accessories.We still have wdk classic for certain things like >boolean/advanced query and history, but I may still need to work on those >to make them fully functional. We are currently into modularising the >components of the browser, so that it can be easily implemented for >different applications.Then it will be released for distribution. > >Sucheta > > > >>Hi Sucheta, >> >>Congrats on the site and DB, looks great. >> >>So, looks like you have used (built) a CGI-based browser instead using >>the WDK (we have been unable to have it completely debugged for the GUS- >>Postgres)... did you give any try to WDK and the GUS-Postgres ? >> >>Looking forward to the public release of your browser. >> >>Cheers, Alberto >> >> >>On Mon, 2005-04-04 at 16:11 -0400, Sucheta Tripathy wrote: >> >> >>>Dear Group, >>> >>>I just wanted to inform you that we have released our phytophthraDB >>>based >>>on GUS. Steve, if you would like to mention in your paper. >>> >>>We have built a brand new browser on the top of GUS database and also >>>have >>>lots of additional features including a community annotation interface. >>>You >>>may check it out at: >>> >>>http://phytophthora.vbi.vt.edu/ >>> >>>The browser will be shortly released after licensing. Thank you all for >>>the >>>support. >>> >>>Sucheta >>> >>>At 10:45 AM 4/4/2005 -0400, Steve Fischer wrote: >>> >>> >>>>GUS users- >>>> >>>>Attached is a draft of a paper describing the GUS system. We have not >>>> >>>> >>>yet >>> >>> >>>>finalized what journal we'll be submitting it to. >>>> >>>>We would like your feedback on the paper before we submit it. >>>> >>>>Also, there is a chart in the paper describing GUS users. Please >>>> >>>> >>>confirm >>> >>> >>>>the information there that is pertinent to you. If you are not in the >>>>chart and would like to be, please provide the necessary information. >>>> >>>> >>>If >>> >>> >>>>you are on the chart and would like to be removed, please let me know. >>>> >>>>Thanks in advance for your feedback, >>>>Steve >>>> >>>> >>>> >>>> > > > > |
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From: Sucheta T. <su...@vb...> - 2005-04-05 12:59:55
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Hi Alberto, We had wdk classic installed for the frontend, but somehow we could not make it work the way we wanted. So we built our cgi based browser, and other accessories.We still have wdk classic for certain things like boolean/advanced query and history, but I may still need to work on those to make them fully functional. We are currently into modularising the components of the browser, so that it can be easily implemented for different applications.Then it will be released for distribution. Sucheta > Hi Sucheta, > > Congrats on the site and DB, looks great. > > So, looks like you have used (built) a CGI-based browser instead using > the WDK (we have been unable to have it completely debugged for the GUS- > Postgres)... did you give any try to WDK and the GUS-Postgres ? > > Looking forward to the public release of your browser. > > Cheers, Alberto > > > On Mon, 2005-04-04 at 16:11 -0400, Sucheta Tripathy wrote: >> Dear Group, >> >> I just wanted to inform you that we have released our phytophthraDB >> based >> on GUS. Steve, if you would like to mention in your paper. >> >> We have built a brand new browser on the top of GUS database and also >> have >> lots of additional features including a community annotation interface. >> You >> may check it out at: >> >> http://phytophthora.vbi.vt.edu/ >> >> The browser will be shortly released after licensing. Thank you all for >> the >> support. >> >> Sucheta >> >> At 10:45 AM 4/4/2005 -0400, Steve Fischer wrote: >> >GUS users- >> > >> >Attached is a draft of a paper describing the GUS system. We have not >> yet >> >finalized what journal we'll be submitting it to. >> > >> >We would like your feedback on the paper before we submit it. >> > >> >Also, there is a chart in the paper describing GUS users. Please >> confirm >> >the information there that is pertinent to you. If you are not in the >> >chart and would like to be, please provide the necessary information. >> If >> >you are on the chart and would like to be removed, please let me know. >> > >> >Thanks in advance for your feedback, >> >Steve >> > >> > > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
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From: Steve F. <sfi...@pc...> - 2005-04-05 12:54:25
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Alberto- Please don't reject the WDK because of postgres bugs. i can work with you to fix them this week. (I'm sorry, i didn't realize you were having that problem.) i have already had a student here use the wdk with postgres. also, any day now the UGA folks will be making CryptoDB public, which is the first site to use the new WDK. You can talk to them to get their evaluation of the WDK. (i am pretty sure they really like it) steve Alberto Davila wrote: >Hi Sucheta, > >Congrats on the site and DB, looks great. > >So, looks like you have used (built) a CGI-based browser instead using >the WDK (we have been unable to have it completely debugged for the GUS- >Postgres)... did you give any try to WDK and the GUS-Postgres ? > >Looking forward to the public release of your browser. > >Cheers, Alberto > > >On Mon, 2005-04-04 at 16:11 -0400, Sucheta Tripathy wrote: > > >>Dear Group, >> >>I just wanted to inform you that we have released our phytophthraDB based >>on GUS. Steve, if you would like to mention in your paper. >> >>We have built a brand new browser on the top of GUS database and also have >>lots of additional features including a community annotation interface. You >>may check it out at: >> >>http://phytophthora.vbi.vt.edu/ >> >>The browser will be shortly released after licensing. Thank you all for the >>support. >> >>Sucheta >> >>At 10:45 AM 4/4/2005 -0400, Steve Fischer wrote: >> >> >>>GUS users- >>> >>>Attached is a draft of a paper describing the GUS system. We have not yet >>>finalized what journal we'll be submitting it to. >>> >>>We would like your feedback on the paper before we submit it. >>> >>>Also, there is a chart in the paper describing GUS users. Please confirm >>>the information there that is pertinent to you. If you are not in the >>>chart and would like to be, please provide the necessary information. If >>>you are on the chart and would like to be removed, please let me know. >>> >>>Thanks in advance for your feedback, >>>Steve >>> >>> >>> >>> |
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From: Alberto D. <da...@io...> - 2005-04-05 12:47:25
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Hi Sucheta, Congrats on the site and DB, looks great. So, looks like you have used (built) a CGI-based browser instead using the WDK (we have been unable to have it completely debugged for the GUS- Postgres)... did you give any try to WDK and the GUS-Postgres ? Looking forward to the public release of your browser. Cheers, Alberto On Mon, 2005-04-04 at 16:11 -0400, Sucheta Tripathy wrote: > Dear Group, > > I just wanted to inform you that we have released our phytophthraDB based > on GUS. Steve, if you would like to mention in your paper. > > We have built a brand new browser on the top of GUS database and also have > lots of additional features including a community annotation interface. You > may check it out at: > > http://phytophthora.vbi.vt.edu/ > > The browser will be shortly released after licensing. Thank you all for the > support. > > Sucheta > > At 10:45 AM 4/4/2005 -0400, Steve Fischer wrote: > >GUS users- > > > >Attached is a draft of a paper describing the GUS system. We have not yet > >finalized what journal we'll be submitting it to. > > > >We would like your feedback on the paper before we submit it. > > > >Also, there is a chart in the paper describing GUS users. Please confirm > >the information there that is pertinent to you. If you are not in the > >chart and would like to be, please provide the necessary information. If > >you are on the chart and would like to be removed, please let me know. > > > >Thanks in advance for your feedback, > >Steve > > > > |
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From: Sucheta T. <su...@vb...> - 2005-04-04 20:11:22
|
Dear Group, I just wanted to inform you that we have released our phytophthraDB based on GUS. Steve, if you would like to mention in your paper. We have built a brand new browser on the top of GUS database and also have lots of additional features including a community annotation interface. You may check it out at: http://phytophthora.vbi.vt.edu/ The browser will be shortly released after licensing. Thank you all for the support. Sucheta At 10:45 AM 4/4/2005 -0400, Steve Fischer wrote: >GUS users- > >Attached is a draft of a paper describing the GUS system. We have not yet >finalized what journal we'll be submitting it to. > >We would like your feedback on the paper before we submit it. > >Also, there is a chart in the paper describing GUS users. Please confirm >the information there that is pertinent to you. If you are not in the >chart and would like to be, please provide the necessary information. If >you are on the chart and would like to be removed, please let me know. > >Thanks in advance for your feedback, >Steve > > > |
|
From: Steve F. <sfi...@pc...> - 2005-04-04 14:45:27
|
GUS users- Attached is a draft of a paper describing the GUS system. We have not yet finalized what journal we'll be submitting it to. We would like your feedback on the paper before we submit it. Also, there is a chart in the paper describing GUS users. Please confirm the information there that is pertinent to you. If you are not in the chart and would like to be, please provide the necessary information. If you are on the chart and would like to be removed, please let me know. Thanks in advance for your feedback, Steve |
|
From: Steve F. <sfi...@pc...> - 2005-04-01 22:33:41
|
ok. but, you'll need java compiling if you want to use the WDK. steve Doma, Narsimha R. (Contr) wrote: >Hi Steve and Mike, > >Thanks for all your help in this process the good news is we could install the plain vanilla version of the GUS platform with in 5 hours this time (second time) as it's given lot of problems first time ... > >a quick update on the problem > >we have to use -skipJavaCompiling option for build command > >build GUS install -append -skipJavaCompiling > >and gus.profile file it only accepting the lower case letter so better we give a update on this with in the install document >I have to change the gus.profile file and database entries to lower case then it works fine. > >I could register the GA and SubmittRow plug in (however it gave me the error for Submitrow with out -commit option with the a insufficient parameters error) once I add the --commit to the process it works fine FYI > >We are planning to do the dataloads and rest of the install process after we get the clear understanding on the vanilla version of the GUS. will update you all the same > >Thanks >Narsimha > >-----Original Message----- >From: Narsimha Reddy [mailto:nr...@ya...] >Sent: Friday, April 01, 2005 3:34 PM >To: Doma, Narsimha R. (Contr); Lancaon, Johanan >Subject: ga +meta -commit output and SubmitRow > > >[domana@rdevse01 gushome]$ ga +meta -commit > <Core::Algorithm> > <name>GA-Plugin</name> > <description>GUS application framework for >plugins</description> > <Core::AlgorithmImplementation> > <cvs_revision>1.53</cvs_revision> > <cvs_tag> </cvs_tag> > ><executable>GUS::PluginMgr::GusApplication</executable> > ><executable_md5>5a2d7e836b14d54027e90f4e8f174fec</executable_md5> > <description>update for GUS 3.0</description> > <Core::AlgorithmInvocation> > <start_time>SYSDATE</start_time> > <end_time>SYSDATE</end_time> > <machine_id>0</machine_id> > <cpus_used>1</cpus_used> > <result>meta</result> > </Core::AlgorithmInvocation> > </Core::AlgorithmImplementation> > </Core::Algorithm> > <Core::Algorithm> > <algorithm_id>21</algorithm_id> > <name>GA-Plugin</name> > <description>GUS application framework for >plugins</description> > <modification_date>SYSDATE</modification_date> > <Core::AlgorithmImplementation> > ><algorithm_implementation_id>21</algorithm_implementation_id> > <algorithm_id>21</algorithm_id> > <cvs_revision>1.53</cvs_revision> > <cvs_tag> </cvs_tag> > ><executable>GUS::PluginMgr::GusApplication</executable> > ><executable_md5>5a2d7e836b14d54027e90f4e8f174fec</executable_md5> > <description>update for GUS 3.0</description> > <modification_date>SYSDATE</modification_date> > <Core::AlgorithmInvocation> > ><algorithm_invocation_id>21</algorithm_invocation_id> > ><algorithm_implementation_id>21</algorithm_implementation_id> > <start_time>SYSDATE</start_time> > <end_time>SYSDATE</end_time> > <machine_id>0</machine_id> > <cpus_used>1</cpus_used> > <result>meta</result> > <modification_date>SYSDATE</modification_date> > <user_read>1</user_read> > <user_write>1</user_write> > <group_read>1</group_read> > <group_write>1</group_write> > <other_read>1</other_read> > <other_write>0</other_write> > <row_user_id>1</row_user_id> > <row_group_id>1</row_group_id> > <row_project_id>1</row_project_id> > ><row_alg_invocation_id>1</row_alg_invocation_id> > </Core::AlgorithmInvocation> > <user_read>1</user_read> > <user_write>1</user_write> > <group_read>1</group_read> > <group_write>1</group_write> > <other_read>1</other_read> > <other_write>0</other_write> > <row_user_id>1</row_user_id> > <row_group_id>1</row_group_id> > <row_project_id>1</row_project_id> > <row_alg_invocation_id>1</row_alg_invocation_id> > </Core::AlgorithmImplementation> > <user_read>1</user_read> > <user_write>1</user_write> > <group_read>1</group_read> > <group_write>1</group_write> > <other_read>1</other_read> > <other_write>0</other_write> > <row_user_id>1</row_user_id> > <row_group_id>1</row_group_id> > <row_project_id>1</row_project_id> > <row_alg_invocation_id>1</row_alg_invocation_id> > </Core::Algorithm> >[domana@rdevse01 gushome]$ > >[domana@rdevse01 gushome]$ ga +create >GUS::Common::Plugin::SubmitRow --commit >Thu Mar 31 15:37:22 2005 INFO Plugin >GUS::Common::Plugin::SubmitRow registered with cvs >revision '1.9' and cvs tag ' ' > > > > |
|
From: Doma, N. R. \(Contr\) <Nar...@ng...> - 2005-04-01 20:58:32
|
Hi Steve and Mike,
Thanks for all your help in this process the good news is we could =
install the plain vanilla version of the GUS platform with in 5 hours =
this time (second time) as it's given lot of problems first time ...
a quick update on the problem
we have to use -skipJavaCompiling option for build command
build GUS install -append -skipJavaCompiling
and gus.profile file it only accepting the lower case letter so better =
we give a update on this with in the install document
I have to change the gus.profile file and database entries to lower case =
then it works fine.
I could register the GA and SubmittRow plug in (however it gave me the =
error for Submitrow with out -commit option with the a insufficient =
parameters error) once I add the --commit to the process it works fine =
FYI
We are planning to do the dataloads and rest of the install process =
after we get the clear understanding on the vanilla version of the GUS. =
will update you all the same=20
Thanks
Narsimha
-----Original Message-----
From: Narsimha Reddy [mailto:nr...@ya...]
Sent: Friday, April 01, 2005 3:34 PM
To: Doma, Narsimha R. (Contr); Lancaon, Johanan
Subject: ga +meta -commit output and SubmitRow
[domana@rdevse01 gushome]$ ga +meta -commit
<Core::Algorithm>
<name>GA-Plugin</name>
<description>GUS application framework for
plugins</description>
<Core::AlgorithmImplementation>
<cvs_revision>1.53</cvs_revision>
<cvs_tag> </cvs_tag>
=20
<executable>GUS::PluginMgr::GusApplication</executable>
=20
<executable_md5>5a2d7e836b14d54027e90f4e8f174fec</executable_md5>
<description>update for GUS 3.0</description>
<Core::AlgorithmInvocation>
<start_time>SYSDATE</start_time>
<end_time>SYSDATE</end_time>
<machine_id>0</machine_id>
<cpus_used>1</cpus_used>
<result>meta</result>
</Core::AlgorithmInvocation>
</Core::AlgorithmImplementation>
</Core::Algorithm>
<Core::Algorithm>
<algorithm_id>21</algorithm_id>
<name>GA-Plugin</name>
<description>GUS application framework for
plugins</description>
<modification_date>SYSDATE</modification_date>
<Core::AlgorithmImplementation>
=20
<algorithm_implementation_id>21</algorithm_implementation_id>
<algorithm_id>21</algorithm_id>
<cvs_revision>1.53</cvs_revision>
<cvs_tag> </cvs_tag>
=20
<executable>GUS::PluginMgr::GusApplication</executable>
=20
<executable_md5>5a2d7e836b14d54027e90f4e8f174fec</executable_md5>
<description>update for GUS 3.0</description>
<modification_date>SYSDATE</modification_date>
<Core::AlgorithmInvocation>
=20
<algorithm_invocation_id>21</algorithm_invocation_id>
=20
<algorithm_implementation_id>21</algorithm_implementation_id>
<start_time>SYSDATE</start_time>
<end_time>SYSDATE</end_time>
<machine_id>0</machine_id>
<cpus_used>1</cpus_used>
<result>meta</result>
<modification_date>SYSDATE</modification_date>
<user_read>1</user_read>
<user_write>1</user_write>
<group_read>1</group_read>
<group_write>1</group_write>
<other_read>1</other_read>
<other_write>0</other_write>
<row_user_id>1</row_user_id>
<row_group_id>1</row_group_id>
<row_project_id>1</row_project_id>
=20
<row_alg_invocation_id>1</row_alg_invocation_id>
</Core::AlgorithmInvocation>
<user_read>1</user_read>
<user_write>1</user_write>
<group_read>1</group_read>
<group_write>1</group_write>
<other_read>1</other_read>
<other_write>0</other_write>
<row_user_id>1</row_user_id>
<row_group_id>1</row_group_id>
<row_project_id>1</row_project_id>
<row_alg_invocation_id>1</row_alg_invocation_id>
</Core::AlgorithmImplementation>
<user_read>1</user_read>
<user_write>1</user_write>
<group_read>1</group_read>
<group_write>1</group_write>
<other_read>1</other_read>
<other_write>0</other_write>
<row_user_id>1</row_user_id>
<row_group_id>1</row_group_id>
<row_project_id>1</row_project_id>
<row_alg_invocation_id>1</row_alg_invocation_id>
</Core::Algorithm>
[domana@rdevse01 gushome]$
[domana@rdevse01 gushome]$ ga +create
GUS::Common::Plugin::SubmitRow --commit
Thu Mar 31 15:37:22 2005 INFO Plugin
GUS::Common::Plugin::SubmitRow registered with cvs
revision '1.9' and cvs tag ' '
|
|
From: Y. T. G. <yon...@pc...> - 2005-04-01 15:25:18
|
Hi Mark, The short answer is: yes we *did* have a plugin CalculateGeneFeatureSeqOverlaps.pm. I do not know why but it (and also a CalculateGeneFeatureESTOverlaps.pm plugin) is now in our legacy cvs repository. Probably we did not think the plugin is of general interest so we did not include it in public release. Here is how I found it out in our GUS instance and it is a great example of how you use the tracking capabilities of GUS. 1) find out if anything is in dots.GeneFeatureSeqOverlap 2) find out who populated it with what algorithm invocations for what projects (in this case Jonathan Schug had one run for GUS project, Jonathan Crabtree, who is no longer at CBIL, had 4 runs each for GUS project and Plasmodium-4.0 project) 3) find out the algorithm implementation id(s) for by row_alg_invocation_id 4) find out the algorithm id(s) for the algorithm implementation id(s) 5) find the algorithm name(s) by id -Thomas On Wed, 30 Mar 2005, Mark S. Heiges wrote: > > I loaded some est BLAT alignments dots.blatalignment with LoadBLATAlignment > (ver 1.32) (how many times can I write blat alignment in one sentence?). > > My dots.GeneFeatureSeqOverlap table is empty and I'm thinking there should > be data there because it's a child of blatalignment, PlasmoDB uses it and > GFSO looks more usable than BA for finding est/gene overlaps. Although, since > I aligned ests against whole contigs instead of individual sequences maybe > GFSO won't help me. > > Is there a plugin to populate GFSO? > > Thanks, > Mark > > > > ------------------------------------------------------- > This SF.net email is sponsored by Demarc: > A global provider of Threat Management Solutions. > Download our HomeAdmin security software for free today! > http://www.demarc.com/Info/Sentarus/hamr30 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Steve F. <sfi...@pc...> - 2005-04-01 15:06:54
|
federica- 1.4 is required. i believe the problem is that there is another version of xerces in the classpath somehow. did you make sure CLASSPATH was empty? can you do this, and send the result: % ls $GUS_HOME/lib/java steve fed...@bi... wrote: >Hi guys! >My problem with wdkXml has not been solved yet! Thanks Steve for your advice! >Now my question is: with GUS WDK 1.2 the requirements of Gus are always >the same? >In particular, what is the j2sdk version required? >Thanks everyone, >Federica > > > >>federica- >> >>the wdk does not need the CLASSPATH to be set. the build takes care of >>that. try emptying your CLASSPATH >> >>steve >> >>fed...@bi... wrote: >> >> >> >>>Hi! It's Federica here, I wrote you in the past! >>>I'm fighting with the wdk model (WDK 1.2)! When I run this command: >>>wdkXml -model toyModel >>> >>>it gives me this java class error: >>>.Exception in thread "main" java.lang.NoSuchMethodError: >>>org.apache.xerces.parser >>>s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >>>nt;)V >>> at >>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>Source) >>> at >>>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>>Source) >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>>Method) >>> at >>>sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >>>orAccessorImpl.java:39) >>> at >>>sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >>>onstructorAccessorImpl.java:27) >>> at >>>java.lang.reflect.Constructor.newInstance(Constructor.java:274) >>> at java.lang.Class.newInstance0(Class.java:308) >>> at java.lang.Class.newInstance(Class.java:261) >>> at >>>org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 >>> 07) >>> at >>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>> 177) >>> at >>>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >>> 137) >>> at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) >>> at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) >>> at >>>org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) >>> at >>>org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac >>> toryImpl.java:95) >>> at >>>com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk >>> nown Source) >>> at >>>com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow >>> n Source) >>> at >>>com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >>>Sourc e) >>> at >>>org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode >>> lXmlParser.java:184) >>> at >>>org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX >>> mlParser.java:71) >>> at >>>org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser >>> .java:412) >>> >>>I think my classpath is correct. In it I specified the path of >>>xercesImpl.jar that should be the archive of my class. >>>Can anyone help me? >>>Thanks >>>Federica >>> >>> >>> >>>------------------------------------------------------- >>>This SF.net email is sponsored by Demarc: >>>A global provider of Threat Management Solutions. >>>Download our HomeAdmin security software for free today! >>>http://www.demarc.com/Info/Sentarus/hamr30 >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> > > > |
|
From: <fed...@bi...> - 2005-04-01 14:26:40
|
Hi guys! My problem with wdkXml has not been solved yet! Thanks Steve for your advice! Now my question is: with GUS WDK 1.2 the requirements of Gus are always the same? In particular, what is the j2sdk version required? Thanks everyone, Federica > federica- > > the wdk does not need the CLASSPATH to be set. the build takes care of > that. try emptying your CLASSPATH > > steve > > fed...@bi... wrote: > >>Hi! It's Federica here, I wrote you in the past! >>I'm fighting with the wdk model (WDK 1.2)! When I run this command: >>wdkXml -model toyModel >> >>it gives me this java class error: >>.Exception in thread "main" java.lang.NoSuchMethodError: >>org.apache.xerces.parser >>s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >>nt;)V >> at >>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>Source) >> at >>org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >>Source) >> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >>Method) >> at >>sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >>orAccessorImpl.java:39) >> at >>sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >>onstructorAccessorImpl.java:27) >> at >> java.lang.reflect.Constructor.newInstance(Constructor.java:274) >> at java.lang.Class.newInstance0(Class.java:308) >> at java.lang.Class.newInstance(Class.java:261) >> at >>org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 >> 07) >> at >>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >> 177) >> at >>org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: >> 137) >> at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) >> at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) >> at >>org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) >> at >>org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac >> toryImpl.java:95) >> at >>com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk >> nown Source) >> at >>com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow >> n Source) >> at >> com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >>Sourc e) >> at >>org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode >> lXmlParser.java:184) >> at >>org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX >> mlParser.java:71) >> at >>org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser >> .java:412) >> >>I think my classpath is correct. In it I specified the path of >>xercesImpl.jar that should be the archive of my class. >>Can anyone help me? >>Thanks >>Federica >> >> >> >>------------------------------------------------------- >>This SF.net email is sponsored by Demarc: >>A global provider of Threat Management Solutions. >>Download our HomeAdmin security software for free today! >>http://www.demarc.com/Info/Sentarus/hamr30 >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > |
|
From: Steve F. <sfi...@pc...> - 2005-03-31 16:14:00
|
federica- the wdk does not need the CLASSPATH to be set. the build takes care of that. try emptying your CLASSPATH steve fed...@bi... wrote: >Hi! It's Federica here, I wrote you in the past! >I'm fighting with the wdk model (WDK 1.2)! When I run this command: >wdkXml -model toyModel > >it gives me this java class error: >.Exception in thread "main" java.lang.NoSuchMethodError: >org.apache.xerces.parser >s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone >nt;)V > at >org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >Source) > at >org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown >Source) > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >Method) > at >sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct >orAccessorImpl.java:39) > at >sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC >onstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > at java.lang.Class.newInstance0(Class.java:308) > at java.lang.Class.newInstance(Class.java:261) > at >org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3 > 07) > at >org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: > 177) > at >org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java: > 137) > at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140) > at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125) > at >org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102) > at >org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac > toryImpl.java:95) > at >com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk > nown Source) > at >com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow > n Source) > at com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown >Sourc e) > at >org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode > lXmlParser.java:184) > at >org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX > mlParser.java:71) > at >org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser > .java:412) > >I think my classpath is correct. In it I specified the path of >xercesImpl.jar that should be the archive of my class. >Can anyone help me? >Thanks >Federica > > > >------------------------------------------------------- >This SF.net email is sponsored by Demarc: >A global provider of Threat Management Solutions. >Download our HomeAdmin security software for free today! >http://www.demarc.com/Info/Sentarus/hamr30 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: <fed...@bi...> - 2005-03-31 14:29:46
|
Hi! It's Federica here, I wrote you in the past!
I'm fighting with the wdk model (WDK 1.2)! When I run this command:
wdkXml -model toyModel
it gives me this java class error:
.Exception in thread "main" java.lang.NoSuchMethodError:
org.apache.xerces.parser
s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone
nt;)V
at
org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown
Source)
at
org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown
Source)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct
orAccessorImpl.java:39)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC
onstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:274)
at java.lang.Class.newInstance0(Class.java:308)
at java.lang.Class.newInstance(Class.java:261)
at
org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3
07)
at
org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java:
177)
at
org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java:
137)
at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140)
at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125)
at
org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102)
at
org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac
toryImpl.java:95)
at
com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk
nown Source)
at
com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow
n Source)
at com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown
Sourc e)
at
org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode
lXmlParser.java:184)
at
org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX
mlParser.java:71)
at
org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser
.java:412)
I think my classpath is correct. In it I specified the path of
xercesImpl.jar that should be the archive of my class.
Can anyone help me?
Thanks
Federica
|
|
From: <fed...@bi...> - 2005-03-31 14:27:45
|
Hi! It's Federica here, I wrote you in the past!
I'm fighting with the wdk model (WDK 1.2)! When I run this command:
wdkXml -model toyModel
it gives me this java class error:
.Exception in thread "main" java.lang.NoSuchMethodError:
org.apache.xerces.parser
s.XML11Configuration.addCommonComponent(Lorg/apache/xerces/xni/parser/XMLCompone
nt;)V
at
org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown
Source)
at
org.apache.xerces.parsers.XIncludeParserConfiguration.<init>(Unknown
Source)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct
orAccessorImpl.java:39)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC
onstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:274)
at java.lang.Class.newInstance0(Class.java:308)
at java.lang.Class.newInstance(Class.java:261)
at
org.apache.xerces.util.ObjectFactory.newInstance(ObjectFactory.java:3
07)
at
org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java:
177)
at
org.apache.xerces.util.ObjectFactory.createObject(ObjectFactory.java:
137)
at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:140)
at org.apache.xerces.parsers.SAXParser.<init>(SAXParser.java:125)
at
org.apache.xerces.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:102)
at
org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFac
toryImpl.java:95)
at
com.thaiopensource.xml.sax.Jaxp11XMLReaderCreator.createXMLReader(Unk
nown Source)
at
com.thaiopensource.validate.auto.AutoSchemaReader.createSchema(Unknow
n Source)
at com.thaiopensource.validate.ValidationDriver.loadSchema(Unknown
Sourc e)
at
org.gusdb.wdk.model.implementation.ModelXmlParser.validModelFile(Mode
lXmlParser.java:184)
at
org.gusdb.wdk.model.implementation.ModelXmlParser.parseXmlFile(ModelX
mlParser.java:71)
at
org.gusdb.wdk.model.implementation.ModelXmlParser.main(ModelXmlParser
.java:412)
I think my classpath is correct. In it I specified the path of
xercesImpl.jar that should be the archive of my class.
Can anyone help me?
Thanks
Federica
|
|
From: Elisabetta M. <man...@pc...> - 2005-03-30 21:33:54
|
I had noticed that too and notified Steve: Date: Wed, 23 Mar 2005 15:52:18 -0500 (EST) From: Elisabetta Manduchi <man...@pc...> To: Steve Fischer <sfi...@pc...> Subject: gusdb link to CVS, changes? Hi Steve, I just went to www.gusdb.org and clicked on the CVS repository link. This took me to Ensembl rather than GUS. I think they changed things there. The following link should take to GUS: http://cvsweb.sanger.ac.uk/cgi-bin/viewcvs.cgi/?root=GUS E. Elisabetta --- On Wed, 30 Mar 2005, Angel Pizarro wrote: > Hello all, > It seems that the cvsweb.sanger.ac.uk defaults to the ensembl project root. > It is not at all clear where GUS files are. After looking around for a minute > or two, I found some pull-down box to specify the "Project Root". But that > was only because I knew what I was looking for and also knew that Sanger has > more than one CVSROOT on that site. > > I suggest to change the GUSDB.org website to update the link to > > http://cvsweb.sanger.ac.uk/cgi-bin/viewcvs.cgi/?root=GUS > from > http://cvsweb.sanger.ac.uk/cgi-bin/viewcvs.cgi/ > > -angel > > -- > > Angel Pizarro > Director, Bioinformatics Facility > Institute for Translational Medicine and Therapeutics > University of Pennsylvania > 806 BRB II/III > 421 Curie Blvd. > Philadelphia, PA 19104-6160 > > P: 215-573-3736 > F: 215-573-9004 > > > > > ------------------------------------------------------- > This SF.net email is sponsored by Demarc: > A global provider of Threat Management Solutions. > Download our HomeAdmin security software for free today! > http://www.demarc.com/Info/Sentarus/hamr30 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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